The company behind Whisper, the social media app that promises users anonymity and claims to be “the safest place on the internet”, is tracking the location of its users, including some who have specifically asked not to be followed.

The practice of monitoring the whereabouts of Whisper users – including those who have expressly opted out of geolocation services – will alarm users, who are encouraged to disclose intimate details about their private and professional lives.

Whisper is also sharing information with the US Department of Defense gleaned from smartphones it knows are used from military bases, and developing a version of its app to conform with Chinese censorship laws.

At the time the company said the story was “not true” and “false”.

Now The Guardian has published a substantial clarification which has been posted at the top of a number of its Whisper stories.

And it has withdrawn from publication altogether an opinion by Guardian journalist James Ball headlined: “Think you can Whisper privately? Think again”.

The clarification says:

Since we published our stories about Whisper between 16 October and 25 October 2014, the company has provided further information.

We confirm that Whisper had drafted the changes to its terms of service and privacy policy before Whisper became aware that the Guardian was intending to write about it. We reported that IP addresses can only provide an approximate indication of a person’s whereabouts, not usually more accurate than their country, state or city.

We are happy to clarify that this data (which all internet companies receive) is a very rough and unreliable indicator of location. We are also happy to make clear that the public cannot ascertain the identity or location of a Whisper user unless the user publicly discloses this information, that the information Whisper shared with the US Department of Defense’s Suicide Prevention Office did not include personal data, and that Whisper did not store data outside the United States.

Whisper’s terms for sharing information proactively with law enforcement authorities where there is a danger of death or serious injury is both lawful and industry standard. The Guardian did not report that any of Whisper’s activities were unlawful. However, we are happy to clarify that there is no evidence for that suggestion.

Whisper contests many other aspects of our reporting.

The Guardian has clarified an article about Whisper’s terms of service and removed an opinion piece entitled “Think you can Whisper privately? Think again”.

The website Techcrunch said in a report: "What seemed fairly damning before, now looks pretty innocuous".